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NC_016162.1__YP_004934229.1__VCYphi_gp07__00007

Bact-Vir

NC_016162.1__YP_004934229.1__VCYphi_gp07__00007

Identity

Accession:
NC_016162 ↗
Kingdom:
phage

Quality

77.4 mean pLDDT

Taxonomy

Loebvirae› Hofneiviricota› Faserviricetes› Tubulavirales› Inoviridae› Vicialiavirus› Vibrio_phage_VCY

TaxID: 1105327

Cluster

View cluster (3 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 48-114
PDB
Domain cluster: rep: OM868077.1__UPT53117.1__X__00008__D36-106
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF10734.15 best DUF2523 33.7 5.90e-08 95.5% 72.5%
CATH (60)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5svlA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.71 57.0 5.70e-01 86.6% 91.2%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.70 49.0 4.07e-01 77.6% 43.8%
3ok8A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.68 51.0 3.51e-01 79.1% 54.3%
3kuqA00 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.67 45.0 3.18e-01 100.0% 24.0%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.67 53.0 5.38e-01 85.1% 89.2%
8a1gC01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.67 48.0 3.53e-01 76.1% 83.4%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.67 52.0 5.04e-01 85.1% 79.7%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 43.0 4.16e-01 70.1% 59.0%
2wdqD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.65 48.0 4.20e-01 80.6% 54.3%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 44.0 3.00e-01 70.1% 21.2%
4nqiD00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.64 48.0 3.26e-01 79.1% 55.2%
2qgnA02 1.10.287.890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain 0.64 48.0 4.50e-01 80.6% 81.7%
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 47.0 4.05e-01 79.1% 50.9%
1sg2A00 3.30.910.20 Alpha Beta › 2-Layer Sandwich › Protein Binding, DinI Protein; Chain A › Skp domain 0.63 54.0 4.33e-01 100.0% 78.0%
7wivA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 50.0 3.26e-01 89.6% 20.5%
1w36B04 1.10.486.10 Mainly Alpha › Orthogonal Bundle › PCRA; domain 4 › PCRA; domain 4 0.62 42.0 3.33e-01 76.1% 32.9%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.62 49.0 4.67e-01 95.5% 72.9%
2vkzA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.62 49.0 3.40e-01 95.5% 23.7%
4mhlA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.62 50.0 3.85e-01 91.0% 95.7%
3idwA00 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.61 30.0 3.10e-01 89.6% 47.0%
6xssA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.61 30.0 3.05e-01 76.1% 46.4%
2oyyA00 6.10.80.10 Special › Helix non-globular › DNA polymerase; domain 1 › Hexameric tyrosine-coordinated heme protein (HTHP) 0.61 53.0 5.22e-01 97.0% 88.7%
2xokP00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.61 45.0 4.42e-01 79.1% 75.7%
2yx8A00 1.10.150.510 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Receptor activity modifying family 0.61 47.0 4.44e-01 83.6% 69.1%
3anwA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 45.0 3.80e-01 79.1% 46.9%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.60 47.0 4.35e-01 85.1% 69.0%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 44.0 3.85e-01 77.6% 68.6%
4lwsB00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.60 44.0 4.03e-01 77.6% 63.6%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.60 45.0 4.29e-01 88.1% 67.1%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.60 47.0 4.02e-01 83.6% 83.8%
4btfA01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.59 38.0 3.35e-01 73.1% 43.0%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.59 49.0 4.01e-01 95.5% 94.8%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.59 46.0 3.73e-01 85.1% 45.9%
4m52A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 52.0 3.63e-01 100.0% 30.6%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 44.0 4.59e-01 83.6% 85.5%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.59 42.0 4.31e-01 77.6% 78.1%
3syvA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.59 45.0 3.14e-01 86.6% 67.8%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 44.0 3.85e-01 83.6% 54.2%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.58 45.0 4.18e-01 83.6% 77.6%
4bx8A03 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.58 42.0 3.63e-01 77.6% 49.1%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.58 42.0 4.36e-01 77.6% 84.4%
4nsmA00 6.10.250.2770 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.58 43.0 4.26e-01 83.6% 74.6%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.58 45.0 4.10e-01 83.6% 64.0%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.57 45.0 4.23e-01 83.6% 75.0%
6a95A01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.57 44.0 3.59e-01 83.6% 84.9%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 40.0 4.21e-01 77.6% 82.0%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 40.0 4.10e-01 80.6% 80.6%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.56 39.0 3.48e-01 76.1% 50.5%
2gl2B00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 43.0 3.67e-01 83.6% 50.5%
2o4cA03 3.30.1370.170 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Erythronate-4-phosphate dehydrogenase, dimerisation domain 0.56 40.0 3.68e-01 76.1% 69.3%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.56 39.0 3.64e-01 82.1% 59.3%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.56 40.0 3.63e-01 79.1% 73.7%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 43.0 4.20e-01 83.6% 87.7%
5dn6J00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.55 41.0 4.04e-01 85.1% 75.7%
4abyD00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 42.0 2.80e-01 86.6% 19.0%
3h3mA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.54 36.0 3.32e-01 74.6% 50.6%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 36.0 3.58e-01 76.1% 64.4%
3hx3A01 1.10.8.20 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p 0.52 35.0 3.58e-01 88.1% 70.1%
4ojmX02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.50 40.0 3.46e-01 86.6% 65.7%
2pmsC00 6.10.140.920 Special › Helix non-globular › Helix Hairpins › 0.50 45.0 3.84e-01 100.0% 95.4%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4336724 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.69 45.0 3.82e-01 71.6% 40.9%
3788311 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.69 46.0 3.83e-01 79.1% 40.0%
5056477 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.67 55.0 5.00e-01 91.0% 67.8%
5006724 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.67 47.0 3.89e-01 73.1% 46.1%
3533309 603.1.1.3 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › V-SNARE 0.66 46.0 3.98e-01 73.1% 49.5%
3917917 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 48.0 4.07e-01 77.6% 50.9%
3959288 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.66 49.0 4.73e-01 83.6% 70.7%
3281725 1075.1.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane 0.65 57.0 3.90e-01 100.0% 60.8%
3786136 603.1.1.3 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › V-SNARE 0.65 46.0 3.83e-01 73.1% 45.2%
3594235 603.1.1.3 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › V-SNARE 0.64 48.0 3.90e-01 79.1% 44.8%
3448821 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.64 49.0 4.12e-01 82.1% 50.0%
4026417 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.63 49.0 4.76e-01 83.6% 78.7%
3284573 150.5.1.11 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › T7SS_ESX_EspC 0.63 49.0 4.28e-01 83.6% 59.0%
5030429 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.63 54.0 4.42e-01 95.5% 53.6%
3503329 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 43.0 3.84e-01 79.1% 49.5%
4039014 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.63 46.0 3.94e-01 77.6% 47.3%
4475138 606.1.1.16 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Transposase_20 0.63 54.0 3.83e-01 95.5% 63.5%
3286299 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.62 45.0 3.87e-01 77.6% 47.3%
3791628 1203.1.2.0 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 0.61 46.0 3.67e-01 83.6% 64.8%
3349325 5086.1.1.135 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › DUF7615 0.61 41.0 3.94e-01 70.1% 66.3%
3512620 3755.4.1.1 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › PI3K_P85_iSH2 0.60 44.0 3.34e-01 77.6% 50.6%
3601853 604.7.1.0 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.60 44.0 3.38e-01 79.1% 35.2%
4939412 4163.1.1.4 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › PF27418 0.60 44.0 3.62e-01 77.6% 66.4%
3991608 109.4.1.102 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › WAPL 0.60 39.0 2.41e-01 73.1% 11.1%
3930099 611.3.1.1 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Med26 0.60 43.0 4.01e-01 79.1% 60.0%
3840064 192.24.1.0 ↗ alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain 0.60 43.0 3.85e-01 76.1% 89.5%
3960219 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.59 46.0 4.43e-01 83.6% 86.7%
3962961 150.5.1.53 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PPE 0.59 43.0 4.03e-01 76.1% 88.7%
3636876 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.59 45.0 3.67e-01 85.1% 99.3%
3940780 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 45.0 3.96e-01 83.6% 63.0%
3240682 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.57 45.0 3.79e-01 83.6% 52.7%
3170876 192.7.1.30 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › CUX1_N 0.57 43.0 3.65e-01 82.1% 47.8%
3596375 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.56 45.0 3.62e-01 85.1% 65.6%
3346986 3711.1.1.4 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › DOG1 0.56 46.0 3.46e-01 100.0% 62.0%
3973899 5086.1.1.92 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_AprE 0.55 43.0 3.43e-01 86.6% 86.9%
4935077 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.55 43.0 4.25e-01 92.5% 81.3%
3929776 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 38.0 2.31e-01 77.6% 9.8%
5012794 4333.1.1.0 ↗ a+b complex topology › DNA methylase specificity domain › DNA methylase specificity domain › DNA methylase specificity domain 0.53 48.0 3.03e-01 100.0% 93.8%
3224003 9001.1.1.3 ↗ alpha bundles › TMEM120/ELO/TLC › TMEM120/ELO/TLC › TMEM120/ELO/TLC › TMPIT 0.53 40.0 3.81e-01 82.1% 77.5%
3503307 1203.1.2.1 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › ASD2 0.53 40.0 3.21e-01 88.1% 86.9%
4276314 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.53 40.0 2.94e-01 86.6% 83.2%
3663565 2498.1.1.10 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M48 0.52 46.0 3.58e-01 100.0% 50.7%
3799718 11.2.1.25 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PL48 0.50 39.0 2.77e-01 91.0% 70.0%